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A Micro-Macro Markov Chain Monte Carlo Method for Molecular Dynamics using Reaction Coordinate Proposals

Journal Contribution - Journal Article

We introduce a new micro-macro Markov chain Monte Carlo method to sample invariant distributions of molecular dynamics systems that exhibit a time-scale separation between the microscopic (fast) dynamics, and the macroscopic (slow) dynamics of some low-dimensional set of reaction coordinates. The algorithm enhances exploration of the state space in the presence of metastability by allowing larger proposed moves at the macroscopic level, on which a conditional accept-reject procedure is applied. Only when the macroscopic proposal is accepted, is the full microscopic state reconstructed from the newly sampled reaction coordinate value and is subjected to a second accept/reject procedure. The computational gain stems from the fact that most proposals are rejected at the macroscopic level, at low computational cost, while microscopic states, once reconstructed, are almost always accepted. We analytically show convergence and discuss the rate of convergence of the proposed algorithm, and numerically illustrate its efficiency on two standard molecular test cases.
Journal: SIAM Journal on Scientific Computing
ISSN: 1064-8275
Issue: 2
Volume: 45
Pages: B107 - B138
Publication year:2023